The H3-3A NM_002107.7:c.103G>A (NP_002098.1:p.(Gly35Arg)) missense variant has not previously been reported in somatic cancers (COSMIC). Based on available guidelines, this variant is considered to be a Variant of Uncertain Significance (VUS).
Five-step scale from benign to pathogenic. This variant is uncertain. Select a step to read what it means.
Uncertain.The recorded classification is uncertain significance.
Gene-level background from the recorded interpretation.
Words with a dotted underline have a short definition. Hover or tap them.H3-3A encodes histone H3.3, a replication-independent protein that is incorporated into chromatin and helps regulate DNA packaging, gene activity, and chromosome organization. It is associated with pediatric glioblastoma and diffuse pontine glioma, where it can contribute to tumor development. H3-3A acts as an oncogene in cancer, with alterations linked to increased tumor growth, invasion, and distinct glioblastoma biology.
The recorded framework is Generic ACMG/AMP 2015 with ClinGen SVI recommendations. The criteria and strengths shown below come from the saved assessment; this page does not recalculate the classification.
The applied criteria and their strengths are shown as assessed under the stated framework.
Met, moderate: Gly35 corresponds to the recurrent H3.3 G34 hotspot, with 18 G34-mutated tumors confined to the G34 molecular subgroup and no supplied benign variation.
Met at supporting: the variant was absent from gnomAD v2.1 and v4.1, well below the <=0.0001 PM2 supporting threshold.
No benign criterion marked as applied in the recorded assessment.
VUS: PM1 (moderate) plus PM2 (supporting) do not meet any generic ACMG/AMP 2015 pathogenic, benign, or likely benign combination rule.
Evidence summaries and captured source records, where available. Missing entries should not be interpreted as negative findings.
gnomAD v4.1 allele counts were not recorded for this variant.
Absent from gnomAD v2.1.
Not available in gnomAD-Canada v1.0.
Recorded REVEL score: 0.443. Refer to the recorded PP3/BP4 rationale for interpretation.
1 other. ClinVar API review status: no assertion criteria provided.
OncoKB identified variant-specific curated literature and context relevant to functional review; biological-effect context: Likely Gain-of-function; curated oncogenicity label: Likely Oncogenic.
This variant has not previously been reported in somatic cancers (COSMIC).
This variant does not lie in a statistically significant hotspot.
ACMG/AMP criteria under Generic ACMG/AMP 2015 with ClinGen SVI recommendations, with the data and sources behind each one.
28 criteria with recorded statuses: 2 met · 8 not met · 14 not assessed · 4 not applicable. Open any row for the full reasoning, the rule and the evidence behind it.
The variant is H3-3A p.Gly35Arg, corresponding to the H3F3A/H3.3 G34R notation used in the literature.
The strongest codon/residue/domain evidence is PM1 at moderate strength because Gly35 corresponds to the recurrent H3.3 G34 mutational hotspot.
PS1 and PM5 are not assessed because the available records do not establish the required pathogenic comparator classifications.
PP2 is not assessed because a low benign-missense rate is not documented, and BP1 is not met because missense disease mechanisms are documented.
No criterion in this group can be assessed because the available evidence contains no proband-level germline parental testing, pedigree, meiosis, segregation, or non-segregation data.
The reviewed publications describe somatic H3F3A/H3-3A G34R/G35R tumor findings and cannot be used as evidence of germline de novo status or familial segregation.
No VCEP covers H3-3A in this case, so the supplied generic ACMG/AMP rules govern.
The reviewed H3F3A/H3.3 G34R literature provides affected-tumor observations but no exact-variant case-control comparison with a calculable OR/RR and 95% CI.
ClinVar does not provide a qualifying exact-variant expert-panel pathogenic, likely pathogenic, benign, or likely benign classification.
This missense variant is evaluated through the single generic REVEL path: REVEL 0.443 is below the PP3 supporting cutoff of 0.644 and above the BP4 supporting cutoff of 0.29, so neither criterion is met.
No SpliceAI score is available, and SpliceAI is not used to adjudicate computational evidence for this missense variant; BayesDel is not calibrated for generic ACMG strength assignment.
No criteria match.
The variant affects Gly35 in H3-3A, corresponding to the recurrent H3F3A/H3.3 G34 position used in the cited literature. PMID:23079654 reports recurrent H3F3A mutations affecting the critical amino acids K27 and G34 and found all 18 G34-mutated tumors confined to the G34 molecular subgroup. PMID:22286061 reports recurrent G34R/G34V mutations in paediatric glioblastoma, and PMID:24705251 reports G34R among recurrent H3.3 alterations in paediatric high-grade glioma. These data establish G34/Gly35 as a mutational hotspot relevant to disease biology. The exact variant is absent from gnomAD v2.1 and v4.1, and no benign variation at the hotspot is documented in the supplied evidence.
Located in a mutational hot spot and/or critical and well-established functional domain (e.g. active site of an enzyme) without benign variation.
PM2 is met at supporting strength. NM_002107.7:c.103G>A (H3-3A p.Gly35Arg) was absent from gnomAD v2.1 and v4.1 all-comers datasets and was also reported absent from the available gnomAD v2.1 non-cancer and v3.1 non-cancer datasets. This satisfies the supplied generic PM2 supporting threshold of allele frequency <=0.0001, including complete absence, with no governing VCEP population-source restriction because no VCEP covers H3-3A.
Absent from controls (or at extremely low frequency if recessive) in Exome Sequencing Project, 1000 Genomes or Exome Aggregation Consortium.
The variant is a missense substitution, so the governing generic rule selects the REVEL path only; SpliceAI is not used for missense PP3/BP4. REVEL is 0.443, below the generic PP3 supporting threshold of >=0.644 and therefore does not meet PP3. BayesDel is not used because no generic ACMG-strength calibration is established.
Multiple lines of computational evidence support a deleterious effect on the gene or gene product (conservation, evolutionary, splicing impact, etc.).
The available case context is a glioma/tumor context, and the reviewed literature describes H3F3A/H3.3 G34R in pediatric or other glioblastoma cohorts. Glioblastoma is not a phenotype shown here to be highly specific for a single genetic etiology, and no phenotype or family-history description establishes that this patient's presentation is specific to H3-3A-related disease. The PP4 definition is therefore not satisfied.
Patient’s phenotype or family history is highly specific for a disease with a single genetic etiology.
ClinVar variation 438766 has no expert-panel submission and no pathogenic or likely pathogenic exact-variant classification; its reported classification is other, with no assertion criteria provided. The only listed submissions are laboratory somatic assertions, not an exact-variant ClinVar expert-panel pathogenic/likely pathogenic classification. PP5 is therefore not met.
Reputable source recently reports variant as pathogenic, but the evidence is not available to the laboratory to perform an independent evaluation.
BA1 is not met. NM_002107.7:c.103G>A (H3-3A p.Gly35Arg) was absent from gnomAD v2.1 and gnomAD v4.1, so no allele-frequency observation supports the generic stand-alone threshold of at least 5%. The available evidence also provides no frequency-based reason to override this result.
Allele frequency is above 5% in Exome Sequencing Project, 1000 Genomes or Exome Aggregation Consortium.
BS1 is not met. The variant was absent from gnomAD v2.1 and v4.1, so there is no measured allele frequency greater than expected for the disorder. The generic 1% default cannot be applied without an elevated observed frequency, and no maximum-credible-frequency calculation is needed to resolve a frequency excess here.
Allele frequency is greater than expected for the disorder.
BP1 is not supported because the supplied gene-level evidence identifies missense variation as a recognized disease mechanism for H3-3A/H3F3A, including recurrent H3.3 missense mutations in glioma and reported germline missense variants causing chromatinopathy. The evidence does not show that disease in this gene is caused primarily by truncating variants.
Missense variant in a gene for which primarily truncating variants are known to cause disease.
The variant is a missense substitution, so the governing generic rule selects the REVEL path only; SpliceAI is not used for missense PP3/BP4. REVEL is 0.443, above the BP4 supporting threshold of <=0.29 and within the gray zone, so BP4 is not met. BayesDel is not used because no generic ACMG-strength calibration is established.
Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc)
ClinVar variation 438766 has no expert-panel submission and no benign or likely benign exact-variant classification; its reported classification is other, with no assertion criteria provided. The available laboratory somatic submissions do not qualify as an exact-variant ClinVar expert-panel benign/likely benign classification. BP6 is therefore not met.
Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation.
The variant is NP_002098.1:p.(Gly35Arg), corresponding to the H3F3A/H3.3 G34R notation used in the literature because of a one-residue numbering offset. PMID:22286061 and PMID:24705251 document the same Gly-to-Arg amino-acid change, but the available evidence describes recurrent somatic glioma mutations and does not establish a prior pathogenic classification for G34R/G35R. ClinVar classifies the exact variant as other with no assertion criteria. Therefore, the same-amino-acid observation is present, but the required previously established pathogenic comparator is not confirmed.
Same amino acid change as a previously established pathogenic variant regardless of nucleotide change.
No proband-level germline evidence, pedigree, parental testing, or documented confirmation of both maternity and paternity is available. The literature reviewed reports H3F3A/H3-3A G34R/G35R in somatic pediatric glioma cohorts, but does not establish this variant as a germline de novo finding in a patient with disease and no family history. Therefore PS2 cannot be assessed.
De novo (both maternity and paternity confirmed) in a patient with the disease and no family history.
The reviewed literature reports recurrent H3F3A/H3.3 Gly-to-Arg tumor mutations and associated molecular tumor phenotypes, but it does not provide a validated, variant-specific in vitro or in vivo functional assay for H3-3A p.Gly35Arg (reported as G34R under the alternate numbering). The available studies therefore do not establish an assay result with appropriate controls, biological functional readout, reproducibility, or clinical-laboratory validation sufficient to apply PS3 at any strength.
Well-established in vitro or in vivo functional studies supportive of a damaging effect on the gene or gene product.
The relevant literature reports H3F3A/H3.3 G34R tumors, corresponding to H3-3A p.(G35R) under the documented one-residue numbering offset, in affected glioma cohorts: five G34R samples in the 48-patient pediatric glioblastoma cohort and 18 G34-mutated tumors in the integrated glioblastoma analysis. These are affected-case series without an unaffected or population-control comparison for this exact variant, and gnomAD v2.1 and v4.1 report absence without a numerical control allele count or frequency. Therefore an OR/RR and 95% CI cannot be calculated, and the PS4 requirement is not assessable rather than met.
The prevalence of the variant in affected individuals is significantly increased compared to the prevalence in controls. ... Relative risk (RR) or odds ratio (OR), as obtained from case-control studies, is >5.0 and the confidence interval around the estimate of RR or OR does not include 1.0.
The variant is NM_002107.7:c.103G>A (p.Gly35Arg), but the available evidence does not establish a recessive disorder context, a pathogenic variant in the same individual, or phase showing that the two variants are in trans. The reviewed tumor studies describe H3F3A/H3.3 G34R as a heterozygous somatic mutation and provide no parental, offspring, or other phase data. Therefore PM3 cannot be assessed from the available evidence.
For recessive disorders, detected in trans with a pathogenic variant
The available literature documents other substitutions at the corresponding H3.3 G34 residue, including G34V, but PM5 requires a novel missense change at a residue where a different missense change has been determined to be pathogenic. The supplied evidence does not provide an established pathogenic classification for a specific alternate G34/Gly35 missense variant, and the exact variant's ClinVar record is classified as other without assertion criteria. Therefore, a PM5 comparator cannot be confirmed.
Novel missense change at an amino acid residue where a different missense change determined to be pathogenic has been seen before.
No evidence documents an assumed de novo germline occurrence in a proband. The available variant reports are somatic glioma studies and do not provide a patient-level germline observation, parental testing, or a pedigree from which de novo status could be assumed. Therefore PM6 cannot be assessed.
Assumed de novo, but without confirmation of paternity and maternity.
No family pedigree, affected relatives, informative meioses, or co-segregation observations are provided. The reviewed literature concerns somatic glioma cohorts rather than multiple affected family members. Therefore PP1 cannot be assessed.
Co-segregation with disease in multiple affected family members in a gene definitively known to cause the disease. ... May be used as stronger evidence with increasing segregation data.
The supplied evidence supports that missense variants in H3-3A/H3F3A can cause disease: the reviewed H3-3A/H3-3B chromatinopathy literature summary describes causative missense variants and gain-of-function or dominant-negative effects, while the glioma papers document recurrent missense substitutions. However, no gene-level metric or reference-table result establishing a low rate of benign missense variation is supplied. Both required PP2 components therefore cannot be confirmed under the stated rule.
Missense variant in a gene that has a low rate of benign missense variation and where missense variants are a common mechanism of disease.
BS2 cannot be assessed from the available evidence. No healthy adult individual is documented as carrying this variant in the required genotype state, and the case materials do not establish the relevant disorder's inheritance, expected penetrance, or age of onset needed to interpret a healthy observation.
Observed in a healthy adult individual for a recessive (homozygous), dominant (heterozygous), or X-linked (hemizygous) disorder, with full penetrance expected at an early age.
The reviewed literature contains no validated, variant-specific in vitro or in vivo assay showing that H3-3A p.Gly35Arg has no damaging effect on protein function or splicing. Tumor observations and associated molecular phenotypes cannot establish a benign functional result, and no assay controls, reproducibility data, or clinical-laboratory validation are available for BS3.
Well-established in vitro or in vivo functional studies show no damaging effect on protein function or splicing.
No affected family members, family genotypes, or non-segregation observations are documented. The available literature does not provide a family in which affected individuals lack the variant, so lack of segregation cannot be evaluated. Therefore BS4 cannot be assessed.
Lack of segregation in affected members of a family.
No evidence identifies a pathogenic variant in trans in a fully penetrant dominant disorder or a pathogenic variant in cis in any inheritance pattern. The available publications concern somatic glioblastoma mutations and do not report a qualifying second pathogenic allele or phase; ClinVar likewise provides no usable phase information. Therefore BP2 cannot be assessed.
Observed in trans with a pathogenic variant for a fully penetrant dominant gene/disorder or observed in cis with a pathogenic variant in any inheritance pattern.
The reviewed evidence does not document this exact variant in a case with an alternate molecular basis for disease. The tumor literature reports H3F3A/H3.3 alterations and glioma cohorts, but does not establish an alternate molecular cause for the specific patient's disease. BP5 cannot be assessed from the available evidence.
Variant found in a case with an alternate molecular basis for disease.
PVS1 (ClinGen SVI PVS1 recommendations, PMC6185798, pvs1_generic_framework) applies only to null variant classes — nonsense, frameshift, canonical ±1/2 splice-consensus, translation-initiation-codon loss, and stop-loss variants — each expected to trigger nonsense-mediated decay or otherwise abolish normal protein function. NM_002107.7:c.103G>A in H3-3A is a missense substitution predicted to produce NP_002098.1:p.(Gly35Arg). As a result, no null-variant mechanism (nonsense-mediated decay, truncation, or canonical splice disruption) is triggered by this variant class, so PVS1's structural prerequisite is not met by this variant class. No VCEP criteria specification covers PVS1 for H3-3A, so the generic ACMG/AMP 2015 definition applies. This determination was made deterministically from the variant's consequence class, prior to LLM adjudication.
deterministic_prefilter: requires_null_variant_class
PM4 (Richards et al. 2015, PMID:25741868) applies to protein length changes: in-frame insertions/deletions in a non-repetitive region, or stop-loss variants that extend the protein past the reference stop codon. NM_002107.7:c.103G>A in H3-3A is a missense substitution predicted to produce NP_002098.1:p.(Gly35Arg). As a result, no change in protein length occurs, so there is nothing for this criterion to evaluate, so PM4's structural prerequisite is not met by this variant class. No VCEP criteria specification covers PM4 for H3-3A, so the generic ACMG/AMP 2015 definition applies. This determination was made deterministically from the variant's consequence class, prior to LLM adjudication.
deterministic_prefilter: requires_stop_loss_or_nonrepeat_indel
BP3 (Richards et al. 2015, PMID:25741868) applies to in-frame insertions/deletions located in a repetitive region without a known function. NM_002107.7:c.103G>A in H3-3A is a missense substitution predicted to produce NP_002098.1:p.(Gly35Arg). As a result, the variant does not alter protein length within a repeat region, so there is nothing for this criterion to evaluate, so BP3's structural prerequisite is not met by this variant class. No VCEP criteria specification covers BP3 for H3-3A, so the generic ACMG/AMP 2015 definition applies. This determination was made deterministically from the variant's consequence class, prior to LLM adjudication.
deterministic_prefilter: requires_repeat_region_indel
BP7 (Richards et al. 2015, PMID:25741868) is defined for a synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence and the nucleotide is not highly conserved. NM_002107.7:c.103G>A in H3-3A is a missense substitution predicted to produce NP_002098.1:p.(Gly35Arg). As a result, the encoded protein sequence is altered, so the criterion's silent-variant premise does not hold regardless of any splicing prediction, so BP7's structural prerequisite is not met by this variant class. No VCEP criteria specification covers BP7 for H3-3A, so the generic ACMG/AMP 2015 definition applies. This determination was made deterministically from the variant's consequence class, prior to LLM adjudication.
deterministic_prefilter: requires_synonymous
Every interpreted variant in H3-3A, mapped onto the exon structure of NM_002107.7. Select a row to find it on the plot.
| Protein | Location | Classification | Link |
|---|
Absent from gnomAD v4.1.
Absent from gnomAD v2.1.
Not available in gnomAD-Canada v1.0.
The variant is a missense substitution, so the governing generic rule selects the REVEL path only; SpliceAI is not used for missense PP3/BP4. REVEL is 0.443, below the generic PP3 supporting threshold of >=0.644 and therefore does not meet PP3. BayesDel is not used because no generic ACMG-strength calibration is established.
Multiple lines of computational evidence support a deleterious effect on the gene or gene product (conservation, evolutionary, splicing impact, etc.).
The variant is a missense substitution, so the governing generic rule selects the REVEL path only; SpliceAI is not used for missense PP3/BP4. REVEL is 0.443, above the BP4 supporting threshold of <=0.29 and within the gray zone, so BP4 is not met. BayesDel is not used because no generic ACMG-strength calibration is established.
Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc)
BP7 (Richards et al. 2015, PMID:25741868) is defined for a synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence and the nucleotide is not highly conserved. NM_002107.7:c.103G>A in H3-3A is a missense substitution predicted to produce NP_002098.1:p.(Gly35Arg). As a result, the encoded protein sequence is altered, so the criterion's silent-variant premise does not hold regardless of any splicing prediction, so BP7's structural prerequisite is not met by this variant class. No VCEP criteria specification covers BP7 for H3-3A, so the generic ACMG/AMP 2015 definition applies. This determination was made deterministically from the variant's consequence class, prior to LLM adjudication.
deterministic_prefilter: requires_synonymous
SpliceAI returned NO scores for this variant, so no SpliceAI-based splice prediction is available. This is missing data, NOT evidence of absent splice impact: it must not be used to support BP4 or to argue against PP3/PVS1. Pangolin scores may be present but are not calibrated for PP3/BP4 here. REVEL score = 0.443. BayesDel score = -0.218235.
10 paper records listed. 3 cited in the classification.
two samples changing glycine 34 to arginine (G34R)
Location Results, paragraph describing the initial six tumours with matched germline DNA; Table/Figure 1 and Figure 2
Context Whole-exome sequencing of 48 paediatric glioblastomas, followed by screening of additional glioma samples with molecular and telomere analyses.
A striking finding of this integrated analysis is that H3F3A K27 and G34 mutations were exclusively distributed to the K27 (18/18) and G34 (18/18) clusters, respectively (p < 0.001; Fisher’s exact test) (Figure 1).
Location Results, Integrated Molecular Classification of Glioblastoma; Figure 1 and associated text
Context Integrated glioblastoma cohorts with H3F3A/IDH1 sequencing, DNA methylation, copy-number, gene-expression, immunohistochemistry, ATRX, and alternative-lengthening-of-telomeres analyses.
whereas histone H3 gene mutations encoding p.Gly34Arg or p.Gly34Val occur in pediatric HGGs of the cerebral cortex3–5,17.
Location Introduction, paragraph 2; Figure 1 clinical summary/caption
Context Whole-genome, whole-exome, and/or transcriptome sequencing of 127 paediatric high-grade gliomas from 118 cases.
the G34V pediatric glioblastoma-linked mutation ... leads to inactive enzyme
Results, section ‘Impact of H3K36me2 peptide mutations involved in intermolecular recognition,’ Figure 2F
An equal number were identified in genes that are now becoming routinely tested in the patient’s tumor type (CTNNB1 in 3 medulloblastomas and H3F3A in a glioblastoma) although not at the time of diagnosis.
Results, Tumor WES, paragraph 1
Duplications and deletions below the detection level according to probe coverage and performance, single-nucleotide variants (SNVs) or insertions/deletions (indels) not covered by the platform, gene expression, or epigenetic modifications.
Limitations of CMA
Screenshots represent source records captured during evidence collection. Select one to view the recorded source content.
The evidence statements recorded by the interpretation pipeline. They have not been reinterpreted by the page.
Absent from gnomAD v4.1.
Absent from gnomAD v2.1.
Not available in gnomAD-Canada v1.0.
This variant has been reported in ClinVar as other (1 clinical laboratory). (ClinVarID = 438766)
SpliceAI returned NO scores for this variant, so no SpliceAI-based splice prediction is available. This is missing data, NOT evidence of absent splice impact: it must not be used to support BP4 or to argue against PP3/PVS1. Pangolin scores may be present but are not calibrated for PP3/BP4 here. REVEL score = 0.443. BayesDel score = -0.218235.
OncoKB identified variant-specific curated literature and context relevant to functional review; biological-effect context: Likely Gain-of-function; curated oncogenicity label: Likely Oncogenic.
This variant does not lie in a statistically significant hotspot. This variant has not previously been reported in somatic cancers (COSMIC).
This variant does not lie in a statistically significant hotspot.